As a company standard we have specific part names for Screws, Bolts, Nuts and Washers. I will save as the required company file name within a fastener folder or the assembly folder. When opening assembly files in SolidWorks the default files from the tool box will open having to go in and replace each and everyone of these parts that are utilized in the assembly. This becomes a real pain time and time again and am to a point where it's not worth the time and effort to use the referenced files in tool box.
Is there a way that I can break this connection so that it does not default back to the original toolbox part.
Have you checked into customization of the toolbox parts?
If that is not something you want to do then run "SLDSETDOCPROP.EXE" which is in your "\\SOLIDWORKS\Toolbox\Data Utilities" folder. Set the property state to NO.
Make sure no file in open in SOLIDWORKS while you run this application. This application will set the toolbox parts to normal parts.